The whole ensemble was put under a new Ministry of Cooperation, created in 1961, separate from the Ministry for Overseas Departments and Territories (known as the DOM-TOM) that had previously run them all. The National Interest review asserts that this "Cooperation Ministry, focal point of the new evolving French system in Africa, regarded Foccart both as their "guarantor" and their advocate with de Gaulle. If the General had conceived the apparatus (though in fact some of it simply happened by improvisation), Foccart was the machine minder." [1]

National Interest 's review of his biography goes on with Foccart's admission that the French secret services eliminated the Cameroonian Marxist leader Félix-Roland Moumié in 1960. Furthermore, it quotes "some reports" which "suggested that Foccart and Houphouët spoke on the phone every Wednesday, and there is no doubt that he considered the Ivoirian leader the African centerpiece of his network. They operated together on a number of issues. Interventions such as that in Gabon in 1964 and Chad in 1969 were encouraged by the Foccart-Houphouet tandem. The most significant collaboration between Foccart and Houphouet was the way they tried to persuade de Gaulle to back the Biafran secession from Nigeria in 1967. Despite the pressures they exerted, however, de Gaulle refused to recognize Biafra, and, in retrospect, so guarded and elliptical are some of Foccart's statements that one cannot be sure what he really wanted or expected from de Gaulle at the time."

Foccart was then replaced by president Valéry Giscard d'Estaing (1974–81) with René Journiac, whom he had trained himself. According to National Interest, he was critical of two special operations carried on under Giscard d'Estaing: the fiasco of the mercenary landing in Benin in January 1977 (with which he denies having had any connection, and would not have supported because it was badly conceived and executed); and "Operation Barracuda", the military intervention that deposed Emperor Bokassa in September 1979.

Foccart was then rehabilitated in 1986 by new Premier Chirac as an adviser on African affairs for the two years of the "cohabitation". When Chirac finally made it to the presidency in 1995, Foccart was brought back to the Elysée at the age of eighty-one, in the main because he still had remarkable contacts with African leaders such as President Omar Bongo of Gabon. He would criticize the devaluation of the CFA franc in January 1994 under Balladur's government, a month after Houphouët-Boigny's death.

However, his role was not limited to Africa, as he was also charged by De Gaulle with the secret services and with the following of the elections, in particular concerning the choice of the candidates during the 1960s. The SAC (Service d'Action Civique) helped him for those shady missions. Foccart also admitted in Foccart Parle that relations with the SDECE intelligence agency were his concerns. National Interest observes that "His biographer's claim that General de Gaulle asked Foccart to reorganize the SDECE (in view of the tainting of both the armed forces and the intelligence agencies by the movement for Algerie Francaise) is indirectly confirmed, but there is not a clear picture of the organization of the barbouzes."

Such had been his influence on French colonial and post colonial policy that when he died on March 19, 1997, "For those involved with what has come to be known nowadays as "Françafrique", denoting the special French sphere of influence in Africa, many, along with Albert Bourgi of Jeune Afrique, saw Foccart's death as 'the end of an epoch.' "[1]

The publication of his memoirs under the format of interviews at the end of his life, and the Journal de l'Elysée also published, in which, starting from 1965, Jacques Foccart transcribed his daily meetings with De Gaulle, have proved an invaluable resource for the knowledge of French policies in Africa.

Furthermore, at his trial in 2006, mercenary Bob Denard, who was tried for his 1995 coup d'état in Comoros, alleged that Foccart had supported him.[2]